Contacts of the helix formed by residues 95 - 121 (chain B) in PDB entry 4I1Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 4.0 7.2 - - - -
94B ASP* 1.3 77.8 - - - +
96B HIS* 1.3 58.2 + - - +
97B GLU* 3.1 4.0 - - - +
98B GLU* 3.1 8.4 + - - -
99B LEU* 2.8 30.0 + - - +
234B VAL* 3.6 10.5 - - - +
237B LYS* 3.8 16.6 - - - -
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Residues in contact with HIS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 4.0 16.6 - - + -
89B TYR* 3.2 39.4 + - + -
90B SER 3.3 7.7 + - - +
91B SER* 3.7 32.1 - - - +
93B TRP 3.2 16.1 + - - +
94B ASP 3.2 4.4 + - - -
95B GLY* 1.3 77.2 - - - +
97B GLU* 1.3 66.1 + - + +
99B LEU* 3.4 7.2 + - + +
100B LYS* 3.1 53.5 + - + +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLY* 3.1 1.8 - - - +
96B HIS* 1.3 87.4 - - + +
98B GLU* 1.3 65.0 + - - +
99B LEU 3.1 1.3 - - - -
100B LYS* 3.1 27.0 + - - +
101B ALA* 3.2 12.0 + - - +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLY* 3.1 8.7 + - - +
97B GLU* 1.3 78.2 - - - +
99B LEU* 1.3 63.1 + - - +
101B ALA* 3.2 17.5 + - - +
102B ILE* 3.0 30.2 + - + +
230B ASN* 4.0 21.8 + - + +
234B VAL* 3.8 22.4 - - + -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU* 3.7 30.1 - - + +
86B GLN* 3.8 32.3 - - + +
89B TYR* 3.9 28.3 - - + -
95B GLY 2.8 17.2 + - - +
96B HIS* 3.4 11.4 - - - +
97B GLU 3.1 0.2 - - - -
98B GLU* 1.3 77.1 - - - +
100B LYS* 1.3 61.2 + - - +
102B ILE* 3.1 14.9 + - + +
103B VAL* 3.1 30.9 + - + +
231B LEU* 5.0 3.8 - - + -
234B VAL* 4.1 10.2 - - + +
235B MET* 4.0 13.5 - - + -
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Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 3.7 32.7 + - + +
96B HIS* 3.1 43.5 + - + +
97B GLU* 3.1 23.3 + - - +
99B LEU* 1.3 75.6 - - - +
101B ALA* 1.3 59.6 + - - +
103B VAL* 3.5 3.8 + - - +
104B TRP* 3.2 21.8 + - - +
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLU 3.2 7.4 + - - +
98B GLU* 3.2 24.9 + - - +
100B LYS* 1.3 74.5 - - - +
102B ILE* 1.3 60.1 + - - +
104B TRP* 4.2 8.7 - - + -
105B ASN* 2.5 45.5 + - - +
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 6.3 1.1 - - - -
85B LEU* 6.6 0.2 - - + -
98B GLU* 3.0 28.7 + - + +
99B LEU* 3.1 14.1 + - + +
101B ALA* 1.3 73.2 - - - +
103B VAL* 1.3 70.9 + - + +
105B ASN* 4.5 4.0 - - - +
106B ASN* 2.8 27.2 + - + +
227B LEU* 4.0 23.7 - - + +
230B ASN* 3.7 27.8 - - + +
231B LEU* 3.6 39.7 - - + +
234B VAL* 4.5 10.8 - - + -
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LYS* 6.4 0.7 - - + -
82B SER* 3.7 41.6 + - - +
83B GLU* 4.6 13.7 - - + +
85B LEU* 5.8 0.2 - - + -
86B GLN* 3.8 33.9 - - - +
99B LEU* 3.1 26.3 + - + +
100B LYS 3.8 2.0 - - - +
102B ILE* 1.3 80.2 - - + +
104B TRP* 1.3 65.4 + - - +
106B ASN* 3.3 16.6 + - - +
107B ASP* 3.3 10.0 + - + +
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Residues in contact with TRP 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LYS 3.2 15.3 + - - +
101B ALA* 3.6 8.5 - - + +
103B VAL* 1.3 80.7 - - - +
105B ASN* 1.3 74.6 + - - +
107B ASP* 3.0 24.6 + - + +
108B LEU* 3.1 42.9 + - + +
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA* 2.5 43.0 + - - +
104B TRP* 1.3 86.5 - - - +
106B ASN* 1.3 66.8 + - - +
108B LEU* 4.1 16.4 - - - +
109B LEU* 3.1 30.6 + - + +
227B LEU* 3.7 25.1 - - + +
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Residues in contact with ASN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG* 4.8 8.7 + - - -
78B SER* 3.1 29.1 + - - -
79B LYS* 4.5 3.0 - - - +
82B SER* 4.2 14.7 + - - +
102B ILE* 2.8 26.3 + - + +
103B VAL* 3.3 9.3 + - - +
105B ASN* 1.3 73.3 - - - +
107B ASP* 1.3 61.3 + - - +
109B LEU* 3.2 3.5 + - - +
110B TRP* 3.0 53.7 + - - -
224B MET* 3.5 16.1 - - - +
227B LEU* 3.4 13.2 - - + +
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Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 3.1 22.9 + - - -
79B LYS* 3.0 47.4 + - - +
103B VAL* 3.8 8.4 - - + +
104B TRP* 3.0 13.5 + - + +
106B ASN* 1.3 78.2 + - - +
108B LEU* 1.3 57.7 + - + +
109B LEU 3.0 2.1 + - - -
110B TRP* 3.1 4.7 + - - +
111B GLU* 2.8 39.9 + - - +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B TRP* 3.1 52.9 + - + +
105B ASN* 4.1 20.4 - - - +
107B ASP* 1.3 79.2 - - + +
109B LEU* 1.3 58.6 + - + +
111B GLU* 4.0 7.4 - - - +
112B ASP* 3.1 27.9 + - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN* 3.1 20.8 + - + +
107B ASP 3.0 1.0 - - - -
108B LEU* 1.3 78.0 - - + +
110B TRP* 1.3 63.7 + - - +
111B GLU 3.3 0.2 - - - -
112B ASP* 3.8 9.2 - - + +
113B TYR* 3.0 26.3 + - - +
219B VAL* 6.1 2.2 - - + -
220B PHE* 4.0 8.8 - - + -
223B GLU* 3.7 46.0 - - + +
224B MET* 3.1 33.0 - - + +
227B LEU* 4.0 16.6 - - + -
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Residues in contact with TRP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A MET* 6.2 0.2 - - - -
221A TYR* 5.7 4.9 - - - -
71B VAL* 4.0 31.6 - - + -
74B MET* 3.4 35.9 - - + -
75B HIS* 3.3 48.2 - + + +
78B SER* 3.5 23.1 + - - -
106B ASN* 3.0 45.4 + - - +
107B ASP 3.6 1.3 - - - +
109B LEU* 1.3 75.6 - - - +
111B GLU* 1.3 54.0 + - - +
113B TYR* 3.6 6.7 - + - +
114B GLU* 2.8 40.6 + - - +
220B PHE* 3.6 33.4 - + - -
224B MET* 4.1 7.3 - - + +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 3.3 22.5 - - + -
107B ASP* 2.8 24.3 + - - +
108B LEU* 4.0 7.9 - - - +
110B TRP* 1.3 72.8 - - - +
112B ASP* 1.3 57.8 + - - +
114B GLU* 3.4 17.8 - - - +
115B GLU* 2.8 63.9 + - - +
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Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU 3.1 19.1 + - - +
109B LEU* 3.8 10.6 - - + +
111B GLU* 1.3 76.6 - - - +
113B TYR* 1.3 62.5 + - - +
115B GLU* 3.9 11.8 - - - +
116B LYS* 3.0 65.2 + - - +
219B VAL* 6.0 2.3 - - - +
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Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 3.8 14.9 - - - -
71B VAL* 3.6 37.0 - - + +
109B LEU 3.0 20.4 + - - +
110B TRP* 3.6 6.5 - + - +
112B ASP* 1.3 79.2 + - - +
114B GLU* 1.3 56.0 + - - +
116B LYS* 3.8 3.1 - - - +
117B LEU* 2.9 42.8 + - + +
216B LEU* 4.0 25.8 - - + -
217B ARG* 3.1 40.7 + - + +
220B PHE* 3.6 47.8 - + + -
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 3.6 9.6 - - + +
71B VAL* 3.4 22.2 - - + +
72B LYS* 3.9 34.8 - - + +
75B HIS* 2.4 44.2 + - - +
110B TRP 2.8 20.9 + - - +
111B GLU* 3.4 23.6 - - - +
113B TYR* 1.3 71.4 - - - +
115B GLU* 1.3 66.4 + - - +
117B LEU* 3.4 7.1 + - - +
118B ALA* 3.1 22.2 + - - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLU* 2.8 50.2 + - - +
112B ASP* 3.9 13.0 - - - +
114B GLU* 1.3 72.6 - - + +
116B LYS* 1.3 60.8 + - + +
118B ALA* 3.1 9.9 + - - +
119B ASP* 3.0 25.8 + - - +
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASP* 3.0 48.4 + - - +
113B TYR* 3.9 3.6 - - - +
115B GLU* 1.3 74.2 - - + +
117B LEU* 1.3 56.5 + - - +
119B ASP* 4.4 5.2 - - - +
120B GLN* 2.6 54.3 + - - +
216B LEU* 3.7 30.3 - - + +
219B VAL* 6.0 4.2 - - - +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 3.8 36.8 - - + -
68B LEU* 3.9 17.5 - - + -
71B VAL* 3.8 16.6 - - + -
113B TYR* 2.9 44.3 + - + +
114B GLU* 3.5 5.4 - - - +
115B GLU 3.4 0.2 - - - -
116B LYS* 1.3 75.3 - - - +
118B ALA* 1.3 57.6 + - - +
121B ALA* 2.8 45.4 + - + +
122B VAL* 3.1 9.3 + - + +
213B ILE* 4.1 16.6 - - + -
216B LEU* 3.7 11.3 - - + +
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.2 17.0 - - + +
72B LYS* 5.7 1.6 - - - +
114B GLU 3.1 12.9 + - - +
115B GLU* 3.1 13.0 + - - +
117B LEU* 1.3 72.7 - - - +
119B ASP* 1.3 61.7 + - - +
122B VAL* 3.8 11.5 - - + +
123B ARG* 2.8 30.5 + - - +
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU 3.0 12.2 + - - +
116B LYS* 3.8 7.4 - - - +
118B ALA* 1.3 81.2 - - - +
120B GLN* 1.3 77.9 + - + +
121B ALA 3.2 1.2 + - - -
123B ARG* 3.2 27.3 + - - +
124B THR* 3.3 9.2 + - - -
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LYS* 2.6 43.4 + - - +
119B ASP* 1.3 86.4 + - + +
121B ALA* 1.3 55.8 + - - +
124B THR* 3.1 17.8 + - - +
209B ILE* 4.7 3.1 - - - -
212B ASN* 3.3 49.6 + - + +
215B ASN* 5.9 0.7 - - - +
216B LEU* 3.8 24.8 - - + +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 4.3 9.0 - - + +
117B LEU* 2.8 27.4 + - + +
120B GLN* 1.3 75.1 - - - +
122B VAL* 1.3 68.7 + - + +
123B ARG 3.5 0.9 - - - -
124B THR* 3.8 2.7 - - - -
125B MET* 3.1 27.2 + - - +
209B ILE* 4.4 10.2 - - + +
213B ILE* 4.1 32.3 - - + -
216B LEU* 6.0 0.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il